We estimated the DNA
copy numbers of the 2011 German outbreak strain E. coli
O104:H4 (TY-2482 and LB226692 from BGIftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/)
on Ion Torrent sequencing data. The O104:H4 copy numbers are given in
relation to the copy numbers of the E. coli strain K12
DH10B (from http://www.edgebio.com/services/iontorrent.php,
download instructions at the bottom). As reference genomes, to which
the sequencing reads are mapped, we used E. coli
strains DH10B, 55989, and O157:H7. Including the sequencing data from
K12 strain in our analysis allowed us to separate technical /
biological variations from true copy numbers. For copy number
estimation, we used our probabilistic model cn.MOPS
(http://www.bioinf.jku.at/software/cnmops/cnmops.html)
which has been designed for estimating copy numbers in next
generation sequencing data. cn.MOPS decomposes read count variations
into variation caused by DNA copy numbers and random/noisy
variations.

That
shiga toxin is produced by O104:H4 was reported in
a NatureNews article
(http://www.nature.com/news/2011/110609/full/news.2011.360.html)
from June 9th by Marian
Turner who writes “The bacterium in this outbreak, currently
recognised as strain O104:H4, makes Shiga toxin, which is responsible
for the severe diarrhoea and kidney damage in patients whose E. coli
infections develop into haemolytic uremic syndrome (HUS).”

Our
finding that tellurium resistance genes are present in O104:H4
has also been reported in NatureNews
(http://www.nature.com/news/2011/110602/full/news.2011.345.html)
at June 2nd by Marian
Turner who writes “In addition to the antibiotic-resistance genes,
the bacteria contain a gene for resistance to the mineral tellurite
(tellurium dioxide)”.

In the same article
Marian Turner writes “One telltale sign is that the strain does not
contain the eae gene, which codes for a protein called intimin, an
adhesion protein that allows the bacteria to attach to cells in the
gut” which we also confirmed.

Our findings concerning
β-lactamases are of interest as they tend to make bacteria resistant
to common antibiotics.